mapCells: mapCells

In aertslab/ScoMAP: ScoMAP: Single-Cell Omics Mapping into spatial Axes using Pseudotemporal ordering

Description

Maps cells on a real cells into a virtual map.

Usage

mapCells(
  VM,
  RM,
  target_clusters = NULL,
  nr_bin = 10,
  seed = 123,
  trajectory_list = list()
)

Arguments

VM	Virtual map data frame
RM	Real map data frame. It must contain the following columns: - 'Cell_type': Annotated cell type - 'Landmark': Reference landmark to use. It must be named as the landmarks in the virtual map, or 'None' is the cells will be randomly mapped on the matching spatial cluster. - 'Pseudotime' : Pseudotime value for the cell. Landmark cell type must be included in the trajectory. - 'PosLandmark' : Relative position to the landmark. If it is set to'Before', it means that the landmark is later in pseudotime, if it is set to 'After' it means that the landmark is located earlier in pseudotime. - 'Spatial_cluster': Spatial cluster to which it will be mapped. These clusters must aggree with VM$cluster_annot.
target_clusters	Spatial clusters to map. If NULL, all clusters will be mapped. Default: NULL.
nr_bin	Number of bins in which the pseudotime and spatial map (as distance from landmark) ordering are divided for mapping. Default: 10.
seed	Seed (as assignment is random). Default: 123.
trajectory_list	A list with dataframes with Pseudotime and Poslandmark columns inferred from spatial data

Value

A virtual map data.frame containing the assigned real cell and its information.

Examples

VM_RNA <- mapCells(VM_RNA, RM_RNA, nr_bin=10)

aertslab/ScoMAP documentation built on Oct. 8, 2021, 1:15 a.m.